Kraken: A set of tools for quality control and analysis of high-throughput sequence data

By Matthew P. Davis, Stijn van Dongen, Cei Abreu-Goodger, Nenad Bartonicek, Anton J. Enright. Methods, 2013

406 citations recorded by the source corpus.

New sequencing technologies pose significant challenges in terms of data complexity and magnitude. It is essential that efficient software is developed with performance that scales with this growth in sequence information. Here we present a comprehensive and integrated set of tools for the analysis of data from large scale sequencing experiments. It supports adapter detection and removal, demultiplexing of barcodes, paired-end data, a range of read architectures and the efficient removal of sequence redundancy. Sequences can be trimmed and filtered based on length, quality and complexity. Quality control plots track sequence length, composition and summary statistics with respect to genomic annotation. Several use cases have been integrated into a single streamlined pipeline, including both mRNA and small RNA sequencing experiments. This pipeline interfaces with existing tools for genomic mapping and differential expression analysis.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5ede31cfb571326547f16746587beb104099452f

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In Molecular Biology

Citations in the corpus

Computational and analytical challenges in single-cell transcriptomics (2015, methodology): “At the level of the raw sequence files, bulk RNA-seq quality control tools, such as fastqc or kraken 46 , can be applied (TABLE 1) .”
UMI-tools: modeling sequencing errors in Unique Molecular Identifiers to improve quantification accuracy (2017, positive): “Sample barcodes were verified and removed, and the adapter sequence was removed from the 3 ′ end of reads using the reaper tool from the Kraken package (version 15-065) (Davis et al. 2013) with parameters “ -3p-head-to-tail 2 -3p-prefix 6/2/1 ” .”
AdapterRemoval v2: rapid adapter trimming, identification, and read merging (2016, methodology): “3 with Minion from the Kraken suite of tools [17].”
Design and computational analysis of single-cell RNA-sequencing experiments (2016, positive): “FASTQC [19], Kraken [20], and RNA-SeQC [21] are all popular tools for assessing the quality of raw and mapped reads within an individual sample.”